Cancer Cell Metabolism Gene Database

  Cancer Cell Metabolism Gene DB

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Gene Summary

Phenotypic Information (metabolism pathway, cancer, disease, phenome)

Mutations: SVs, CNVs, SNVs

Gene expression: GE, Protein, DEGE, CNV vs GE

Gene-Gene Network Information: Co-Expression Network, Interacting Genes & KEGG

Pharmacological Information: Drug-Gene Network

Cross referenced IDs

Gene Summary for ADCY3
Basic gene info.Gene symbolADCY3
Gene nameadenylate cyclase 3
SynonymsAC3
CytomapUCSC genome browser: 2p23.3
Genomic locationchr2 :25042038-25142055
Type of geneprotein-coding
RefGenesNM_004036.3,
Ensembl idENSG00000138031
DescriptionAC-IIIATP pyrophosphate-lyase 3adenylate cyclase type 3adenylate cyclase type IIIadenylate cyclase, olfactive typeadenylyl cyclase 3adenylyl cyclase, type III
Modification date20141207
dbXrefs MIM : 600291
HGNC : HGNC
Ensembl : ENSG00000138031
HPRD : 02620
Vega : OTTHUMG00000094765
ProteinUniProt: O60266
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_ADCY3
BioGPS: 109
Gene Expression Atlas: ENSG00000138031
The Human Protein Atlas: ENSG00000138031
PathwayNCI Pathway Interaction Database: ADCY3
KEGG: ADCY3
REACTOME: ADCY3
ConsensusPathDB
Pathway Commons: ADCY3
MetabolismMetaCyc: ADCY3
HUMANCyc: ADCY3
RegulationEnsembl's Regulation: ENSG00000138031
miRBase: chr2 :25,042,038-25,142,055
TargetScan: NM_004036
cisRED: ENSG00000138031
ContextiHOP: ADCY3
cancer metabolism search in PubMed: ADCY3
UCL Cancer Institute: ADCY3
Assigned class in ccmGDBA - This gene has a literature evidence and it belongs to cancer gene.
References showing role of ADCY3 in cancer cell metabolism1. Hong SH, Goh SH, Lee SJ, Hwang JA, Lee J, et al. (2013) Upregulation of adenylate cyclase 3 (ADCY3) increases the tumorigenic potential of cells by activating the CREB pathway. Oncotarget 4: 1791-1803. pmid: 3858564. go to article

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Phenotypic Information for ADCY3(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: ADCY3
Familial Cancer Database: ADCY3
* This gene is included in those cancer gene databases.

.

Oncogene 1

Tumor Suppressor gene 2

Cancer Gene Census 3

CancerGenes 4

Network of Cancer Gene 5

Significant driver gene in

Therapeutic Vulnerabilities in Cancer1

cf) number; DB name
1 Oncogene; http://nar.oxfordjournals.org/content/35/suppl_1/D721.long,
2 Tumor Suppressor gene; https://bioinfo.uth.edu/TSGene/,
3 Cancer Gene Census; http://www.nature.com/nrc/journal/v4/n3/abs/nrc1299.html,
4 CancerGenes; http://nar.oxfordjournals.org/content/35/suppl_1/D721.long,
5 Network of Cancer Gene; http://ncg.kcl.ac.uk/index.php,
1Therapeutic Vulnerabilities in Cancer; http://cbio.mskcc.org/cancergenomics/statius/

check002.gifMetabolic Pathway Description
KEGG_PURINE_METABOLISM
REACTOME_INTEGRATION_OF_ENERGY_METABOLISM

check002.gifOthers
OMIM 600291; gene.
Orphanet
DiseaseKEGG Disease: ADCY3
MedGen: ADCY3 (Human Medical Genetics with Condition)
ClinVar: ADCY3
PhenotypeMGI: ADCY3 (International Mouse Phenotyping Consortium)
PhenomicDB: ADCY3

Mutations for ADCY3
* Under tables are showing count per each tissue to give us broad intuition about tissue specific mutation patterns.You can go to the detailed page for each mutation database's web site.

check002.gifStructural Variants in COSMIC: go to COSMIC mutation histogram

- Statistics for Tissue and Mutation typeTop
- For Inter-chromosomal Variations
There's no inter-chromosomal structural variation.
- For Intra-chromosomal Variations
* Intra-chromosomal variantions includes 'intrachromosomal amplicon to amplicon', 'intrachromosomal amplicon to non-amplified dna', 'intrachromosomal deletion', 'intrachromosomal fold-back inversion', 'intrachromosomal inversion', 'intrachromosomal tandem duplication', 'Intrachromosomal unknown type', 'intrachromosomal with inverted orientation', 'intrachromosomal with non-inverted orientation'.
SampleSymbol_aChr_aStart_aEnd_aSymbol_bChr_bStart_bEnd_b
lungADCY3chr22508109225081092chr22594220925942209
cf) Tissue number; Tissue name (1;Breast, 2;Central_nervous_system, 3;Haematopoietic_and_lymphoid_tissue, 4;Large_intestine, 5;Liver, 6;Lung, 7;Ovary, 8;Pancreas, 9;Prostate, 10;Skin, 11;Soft_tissue, 12;Upper_aerodigestive_tract)

check002.gifRelated fusion transcripts : go to Chitars2.0
* From mRNA Sanger sequences, Chitars2.0 arranged chimeric transcripts. This table shows ADCY3 related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a

check002.gifOther DBs for Structural Variants
Structural Variants in Ensembl: go to Ensembl Structural variation
Structural Variants in dbVar: go to dbVar

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check002.gifCopy Number Variations in COSMIC: go to COSMIC mutation CNV/Expr
 
Mutation type/ Tissue IDbrcacnscervendomehaematopokidnLintestliverlungnsovarypancreprostskinstomathyrourina
Total # sample1     1          
GAIN (# sample)1                
LOSS (# sample)      1          
cf) Tissue ID; Tissue type (1; Breast, 2; Central_nervous_system, 3; Cervix, 4; Endometrium, 5; Haematopoietic_and_lymphoid_tissue, 6; Kidney, 7; Large_intestine, 8; Liver, 9; Lung, 10; NS, 11; Ovary, 12; Pancreas, 13; Prostate, 14; Skin, 15; Stomach, 16; Thyroid, 17; Urinary_tract)

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check002.gifSNV Counts per Each Loci in COSMIC data: go to COSMIC point mutation

 : Non-synonymous mutation, : Synonymous mutation, Circle size denotes number of samples.
Maximum mutation count=3

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check002.gifSomatic Mutation Counts per Tissue in COSMIC data
Stat. for Non-Synonymous SNVs
(# total SNVs=78)
Stat. for Synonymous SNVs
(# total SNVs=43)
Stat. for Deletions
(# total SNVs=2)
Stat. for Insertions
(# total SNVs=0)
There's no inserted snv.

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check002.gifTop 10 SNVs Having the Most Samples in COSMIC data
* When you move the cursor on each content, you can see more deailed mutation information on the Tooltip. Those are primary_site,primary_histology,mutation(aa),pubmedID.
GRCh37 positionMutation(aa)Unique sampleID count
chr2:25095541-25095541p.I241I3
chr2:25141368-25141368p.H163H3
chr2:25141245-25141245p.V204V2
chr2:25141434-25141434p.Y141Y2
chr2:25057470-25057470p.D617D2
chr2:25095482-25095482p.S261L2
chr2:25062756-25062756p.A447A2
chr2:25043615-25043615p.T1077K2
chr2:25062839-25062839p.V420M2
chr2:25043704-25043704p.G1047G2

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check002.gifSNV Counts per Each Loci in TCGA data

 : non-synonymous mutation, : synonymous mutation, Circle size denotes number of samples.
maximum mutation count=2

Point Mutation/ Tissue ID1234567891011121314151617181920
# sample34 162 6 211862  97115
# mutation34 172 6 211872  108115
nonsynonymous SNV22 92 4 211562  16110
synonymous SNV12 8  2    31   92 5
cf) Tissue ID; Tissue type (1; BLCA[Bladder Urothelial Carcinoma], 2; BRCA[Breast invasive carcinoma], 3; CESC[Cervical squamous cell carcinoma and endocervical adenocarcinoma], 4; COAD[Colon adenocarcinoma], 5; GBM[Glioblastoma multiforme], 6; Glioma Low Grade, 7; HNSC[Head and Neck squamous cell carcinoma], 8; KICH[Kidney Chromophobe], 9; KIRC[Kidney renal clear cell carcinoma], 10; KIRP[Kidney renal papillary cell carcinoma], 11; LAML[Acute Myeloid Leukemia], 12; LUAD[Lung adenocarcinoma], 13; LUSC[Lung squamous cell carcinoma], 14; OV[Ovarian serous cystadenocarcinoma ], 15; PAAD[Pancreatic adenocarcinoma], 16; PRAD[Prostate adenocarcinoma], 17; SKCM[Skin Cutaneous Melanoma], 18:STAD[Stomach adenocarcinoma], 19:THCA[Thyroid carcinoma], 20:UCEC[Uterine Corpus Endometrial Carcinoma])

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check002.gifTop 10 SNVs Having the Most Samples in TCGA data
* We represented just top 10 SNVs. When you move the cursor on each content, you can see more deailed mutation information on the Tooltip. Those are primary_site, primary_histology, mutation(aa), pubmedID.
Genomic PositionMutation(aa)Unique sampleID count
chr2:25062839p.A149T2
chr2:25043704p.G1047G2
chr2:25141412p.V420M2
chr2:25048969p.D298D1
chr2:25043682p.A984V1
chr2:25054533p.L777L1
chr2:25095488p.E533K1
chr2:25046099p.H286P1
chr2:25061315p.T135T1
chr2:25141470p.T976I1

check002.gifOther DBs for Point Mutations
Point Mutation Table of Ensembl: go to Ensembl variation table
Mutation of cBioPortal: go to cBioPortal's Cross-cancer alteration summary

check002.gifCopy Number for ADCY3 in TCGA
* Copy number data were extracted from TCGA using R package TCGA-Assembler. The URLs of all public data files on TCGA DCC data server were gathered on Jan-05-2015. Function ProcessCNAData in TCGA-Assembler package was used to obtain gene-level copy number value which is calculated as the average copy number of the genomic region of a gene.
cf) Tissue ID[Tissue type]: BLCA[Bladder Urothelial Carcinoma], BRCA[Breast invasive carcinoma], CESC[Cervical squamous cell carcinoma and endocervical adenocarcinoma], COAD[Colon adenocarcinoma], GBM[Glioblastoma multiforme], Glioma Low Grade, HNSC[Head and Neck squamous cell carcinoma], KICH[Kidney Chromophobe], KIRC[Kidney renal clear cell carcinoma], KIRP[Kidney renal papillary cell carcinoma], LAML[Acute Myeloid Leukemia], LUAD[Lung adenocarcinoma], LUSC[Lung squamous cell carcinoma], OV[Ovarian serous cystadenocarcinoma ], PAAD[Pancreatic adenocarcinoma], PRAD[Prostate adenocarcinoma], SKCM[Skin Cutaneous Melanoma], STAD[Stomach adenocarcinoma], THCA[Thyroid carcinoma], UCEC[Uterine Corpus Endometrial Carcinoma]

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Gene Expression for ADCY3

check002.gifGene Expression in Cancer Cell-lines (CCLE)
* CCLE gene expression data were extracted from CCLE_Expression_Entrez_2012-10-18.res: Gene-centric RMA-normalized mRNA expression data.

check002.gifDifferential Gene Expression in Primary Tumors (TCGA)
* Normalized gene expression data of RNASeqV2 was extracted from TCGA using R package TCGA-Assembler. The URLs of all public data files on TCGA DCC data server were gathered at Jan-05-2015. Only eight cancer types have enough normal control samples for differential expression analysis.
(t test, adjusted p<0.05 (using Benjamini-Hochberg FDR))
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check002.gifCNV vs Gene Expression Plot
* This plots show the correlation between CNV and gene expression.

: Open all plots for all cancer types


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Gene-Gene Network Information
check002.gifCo-Expressed gene's network Plot
* Co-Expression network figures were drawn using R package igraph. Only the top 20 genes with the highest correlations were shown.
Red circle: input gene, orange circle: cell metabolism gene, sky circle: other gene

: Open all plots for all cancer types

ADCY3,CD14,CD180,CSF2RA,DOK5,EDN3,GNLY,
KIR2DL3,LIPG,MRGPRX3,NOS1,PAK3,PDE11A,PGA5,
PTN,TGFBR2,TLR2,TMEM100,TMEM233,VNN1,XDH
ACVRL1,ADCY3,AEBP1,BMP1,C1R,C1S,C3,
CALHM2,CNTNAP1,GLIS2,GNAI2,GRK5,ITGA5,MAN1C1,
MFNG,PLXND1,SYDE1,TMEM119,TMEM173,TNFRSF1A,TNFRSF1B

ADCY3,ASB13,ASXL1,SPATA25,CEP250,DHX35,DNAJC5,
GNG4,KCNAB2,TTI1,NCOA6,PHF20,POLR1A,RNF43,
RPRD1B,STX16,TAF4,TBC1D16,TEX261,TRPC4AP,ZHX3
ADCY3,ARAP3,BICD1,FAM208B,C1QTNF1,CD276,CEP135,
CEP164,CEP97,DDHD1,DPY19L3,ILF3,LOC100129387,MDC1,
NTRK3,NUP188,R3HDM1,RFX7,TP53BP1,UBQLN4,URB1
check002.gifCo-Expressed gene's Protein-protein interaction Network Plot
* Co-Expression network figures were drawn using R package igraph. Only the top 20 genes with the highest correlations were shown.
Red circle: input gene, orange circle: cell metabolism gene, sky circle: other gene

: Open all plots for all cancer types

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check002.gifInteracting Genes (from Pathway Commons)

: Open all interacting genes' information including KEGG pathway for all interacting genes from DAVID

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Pharmacological Information for ADCY3
check002.gifCross-referenced pharmacological DB IDs from Uniprot
DB CategoryDB NameDB's ID and Url link
ChemistryChEMBL CHEMBL2097167; -.
Organism-specific databasesPharmGKB PA164741137; -.
Organism-specific databasesCTD 109; -.

check002.gifDrug-Gene Interaction Network
* Gene Centered Interaction Network.
* Drug Centered Interaction Network.
DrugBank IDTarget NameDrug GroupsGeneric NameDrug Centered NetworkDrug Structure
DB00938adenylate cyclase 3approvedSalmeterol


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Cross referenced IDs for ADCY3
* We obtained these cross-references from Uniprot database. It covers 150 different DBs, 18 categories. http://www.uniprot.org/help/cross_references_section

: Open all cross reference information



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